Research Groups

* joined first author # joined corresponding author

2021

Giulio Formenti#, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane A McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S Horner, Eugene W Myers, Richard Durbin, Alessandro Achilli, Edward L Braun, Adam M Phillippy, Erich D Jarvis#, Erich D null
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
Genome Biol, 22(1) Art. No. 120 (2021)
Open Access   DOI
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Lina Muhandes, Maria Chapsa, Martin Pippel, Rayk Behrendt, Yan Ge, Andreas Dahl, Buqing Yi, Alexander Dalpke, Sylke Winkler, Michael Hiller, Sebastien Boutin, Stefan Beissert, Rolf Jessberger, Padraic G Fallon, Axel Roers
Low threshold for cutaneous allergen sensitization but no spontaneous dermatitis or atopy in filaggrin-deficient mice.
J. Invest. Dermatol., Art. No. doi: 10.1016/j.jid.2021.02.763 (2021)
DOI
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Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L Gedman, Lindsey J Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jonathon Howard, Sonja Vernes, Tanya M Lama, Frank Grutzner, Wesley C Warren, Christopher N Balakrishnan, Dave Burt, Julia M George, Matthew T Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F Kautt, Paolo Franchini, H William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J P Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B Kingan, Richard J Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex R Hastie, Joyce Lee, Siddarth Selvaraj, Richard E Green, Nicholas H Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E Dagnew, Dengfeng Guan, Sarah E London, David F Clayton, Claudio V Mello, Samantha R Friedrich, Peter V Lovell, Ekaterina Osipova, Farooq O Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S Harris, Kateryna D Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kerstin Howe#, Paul Flicek, Brian Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H S Kraus, Andrew J Crawford, M Thomas P Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert F Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A Ryder, David Haussler, Stephen J O'Brien, Jonas Korlach, Harris A Lewin, Kerstin Howe#, Eugene W Myers#, Richard Durbin#, Adam M Phillippy#, Erich D Jarvis#
Towards complete and error-free genome assemblies of all vertebrate species.
Nature, 592(7856) 737-746 (2021)
Open Access   DOI

2020

Peiwen Xiong, C Darrin Hulsey, Carmelo Fruciano, Wai Y Wong, Alexander Nater, Andreas F Kautt, Oleg Simakov, Martin Pippel, Shigehiro Kuraku, Axel Meyer, Paolo Franchini
The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes.
Mol. Ecol., 30(4) 955-972 (2020)
Open Access   DOI
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Yuta Suzuki#, Eugene W Myers, Shinichi Morishita#
Rapid and ongoing evolution of repetitive sequence structures in human centromeres.
Sci Adv, 6(50) Art. No. eabd9230 (2020)
Open Access   DOI
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Andreas F Kautt, Claudius F Kratochwil, Alexander Nater, Gonzalo Machado-Schiaffino, Melisa Olave, Frederico Henning, Julián Torres-Dowdall, Andreas Härer, C Darrin Hulsey, Paolo Franchini, Martin Pippel, Eugene W Myers, Axel Meyer
Contrasting signatures of genomic divergence during sympatric speciation.
Nature, 588(7836) 106-111 (2020)
Open Access   DOI
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Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurelien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert#, Eugene W Myers#
Practical sensorless aberration estimation for 3D microscopy with deep learning.
Opt express, 28(20) 29044-29053 (2020)
Open Access   DOI
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Gautam Dey, Sian Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, Buzz Baum
Closed mitosis requires local disassembly of the nuclear envelope.
Nature, 585(7823) 119-123 (2020)
DOI
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David Jebb✳︎, Zixia Huang✳︎, Martin Pippel✳︎, Graham M Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S Jermiin, Emilia C Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A Ray, Kevin F. Sullivan, Juliana G. Roscito, Bogdan Kirilenko, Liliana M Dávalos, Angelique P Corthals, Megan L Power, Gareth Jones, Roger D Ransome, Dina K N Dechmann, Andrea G Locatelli, Sébastien J Puechmaille, Olivier Fedrigo, Erich D Jarvis, Michael Hiller#, Sonja Vernes#, Eugene W Myers#, Emma Teeling#
Six reference-quality genomes reveal evolution of bat adaptations.
Nature, 583(7817) 578-584 (2020)
Open Access   DOI
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Andre Arashiro Pulschen, Delyan R Mutavchiev, Sian Culley, Kim Nadine Sebastian, Jacques Roubinet, Marc Roubinet, Gabriel Tarrason Risa, Marleen van Wolferen, Chantal Roubinet, Uwe Schmidt, Gautam Dey, Sonja-Verena Albers, Ricardo Henriques, Buzz Baum
Live Imaging of a Hyperthermophilic Archaeon Reveals Distinct Roles for Two ESCRT-III Homologs in Ensuring a Robust and Symmetric Division.
Curr Biol, 30(14) 2852-2859 (2020)
Open Access   DOI
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Coleman Broaddus, Alexander Krull, Martin Weigert, Uwe Schmidt, Gene Myers
Removing Structured Noise with Self-Supervised Blind-Spot Networks.
In: IEEE ISBI 2020 : International Conference on Biomedical Imaging : April 2-7, 2020, Iowa City, Iowa, USA : symposium proceeding (2020) IEEE International Symposium on Biomedical Imaging, Piscataway, N.J., IEEE (2020), 159-163
DOI
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Robert Haase✳︎, Loic Royer✳︎, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, Eugene W Myers
CLIJ: GPU-accelerated image processing for everyone.
Nat Methods, 17(1) 5-6 (2020)
DOI
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Martin Pippel✳︎, David Jebb✳︎, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller#, Anna K Hundsdoerfer#
A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).
GigaScience, 9(1) Art. No. giaa001 (2020)
Open Access   DOI

2019

Kaushikaram Subramanian, Martin Weigert, Oliver Borsch, Heike Petzold, Alfonso Garcia-Ulloa, Eugene W Myers, Marius Ader, Irina Solovei, Moritz Kreysing
Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice.
Elife, 8 Art. No. e49542 (2019)
Open Access   DOI
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Hanh Thi-Kim Vu, Sarah Mansour, Michael Kücken, Corinna Blasse, Claire Basquin, Juliette Azimzadeh, Eugene W Myers, Lutz Brusch#, Jochen Rink#
Dynamic Polarization of the Multiciliated Planarian Epidermis between Body Plan Landmarks.
Dev Cell, 51(4) 526-542 (2019)
DOI
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Christoph Stritt, Michele Wyler, Elena L Gimmi, Martin Pippel, Anne C Roulin
Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon.
New Phytol., 227(6) 1736-1748 (2019)
Open Access   DOI
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Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson, Armin Töpfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M Phillippy, Michael C Schatz, Gene Myers, Mark A DePristo, Jue Ruan, Tobias Marschall, Fritz J Sedlazeck, Justin M Zook, Heng Li, Sergey Koren, Andrew Carroll, David R Rank, Michael W Hunkapiller
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Nat Biotechnol, 37(10) 1155-1162 (2019)
DOI
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Falk Zakrzewski, Walter de Back, Martin Weigert, Torsten Wenke, Silke Zeugner, Robert Mantey, Christian Sperling, Katrin Friedrich, Ingo Roeder, Daniela Aust, Gustavo Baretton, Pia Hönscheid
Automated detection of the HER2 gene amplification status in Fluorescence in situ hybridization images for the diagnostics of cancer tissues.
Sci Rep, 9(1) Art. No. 8231 (2019)
Open Access   DOI
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German Tischler-Höhle
Haplotype and repeat separation in long reads.
In: Computational Intelligence Methods for Bioinformatics and Biostatistics : 14th International Meeting, CIBB 2017, Cagliari, Italy, September 7-9, 2017, Revised Selected Papers (2019)(Eds.) Massimo Bartoletti (Lecture Notes in Computer Science ;10834), Cham, Springer International Publishing (2019), 103-114
DOI

2018

Juliana G. Roscito, Katrin Sameith, Martin Pippel, Kees-Jan Francoijs, Sylke Winkler, Andreas Dahl, Georg Papoutsoglou, Gene Myers, Michael Hiller
The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly.
GigaScience, 7(12) Art. No. giy141 (2018)
Open Access   PDF    DOI
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Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Sian Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W Myers
Content-aware image restoration: pushing the limits of fluorescence microscopy.
Nat Methods, 15(12) 1090-1097 (2018)
DOI
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Liyuan Sui, Silvanus Alt, Martin Weigert, Natalie Dye, Suzanne Eaton, Florian Jug, Eugene W Myers, Frank Jülicher, Guillaume Salbreux, Christian Dahmann
Differential lateral and basal tension drive folding of Drosophila wing discs through two distinct mechanisms.
Nat Commun, 9(1) Art. No. 4620 (2018)
Open Access   DOI
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Uwe Schmidt✳︎, Martin Weigert✳︎, Coleman Broaddus, Gene Myers
Cell Detection with Star-Convex Polygons
In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 : 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part II (2018)(Eds.) Alejandro F. Frangi Lecture Notes in Computer Science ; 11071, Cham, Springer International Publishing (2018), 265-273
DOI
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Djamal Belazzougui, Fabio Cunial, Olgert Denas
Fast matching statistics in small space
In: 17th International Symposium on Experimental Algorithms (SEA 2018) (2018) Ch. 17(Eds.) Gianlorenzo D'Angelo (LIPIcs - Leibniz International Proceedings in Informatics ; Volume 103), Wadern, Schloss Dagstuhl - Leibniz-Zentrum für Informatik GmbH (2018), 1701-1714
DOI
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Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W Myers, Moritz Kreysing
Biobeam-Multiplexed wave-optical simulations of light-sheet microscopy.
PLoS Comput Biol, 14(4) Art. No. e1006079 (2018)
Open Access   PDF    DOI
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Emma Teeling, Sonja Vernes, Liliana M Dávalos, David A Ray, M Thomas P Gilbert, Eugene Myers, Bat1K Consortium
Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.
Annu Rev Anim Biosci, 6 23-46 (2018)
DOI
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Markus Grohme✳︎, Siegfried Schloissnig✳︎, Andrei Rozanski, Martin Pippel, George Robert Young, Sylke Winkler, Holger Brandl, Ian Henry, Andreas Dahl, Sean Powell, Michael Hiller, Eugene Myers, Jochen Rink
The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms.
Nature, 554(7690) 56-61 (2018)
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Sergej Nowoshilow, Siegfried Schloissnig, Jifeng Fei, Andreas Dahl, Andy W C Pang, Martin Pippel, Sylke Winkler, Alex R Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M. Tanaka, Eugene W Myers
The axolotl genome and the evolution of key tissue formation regulators.
Nature, 554(7690) 50-55 (2018)
Open Access   PDF    DOI
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Matthias Kaiser, Florian Jug, Thomas Julou, Siddharth Deshpande, Thomas Pfohl, Olin Silander#, Gene Myers#, Erik van Nimwegen#
Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.
Nat Commun, 9(1) Art. No. 212 (2018)
Open Access   DOI

2017

Jacob Kruse, Carsten Rother, Uwe Schmidt
Learning to Push the Limits of Efficient FFT-based Image Deconvolution
In: 2017 IEEE International Conference on Computer Vision : ICCV 2017 : proceedings : 22-29 October 2017, Venice, Italy (2017), Piscataway, N.J., IEEE (2017), 4596-4604
DOI
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Markus Rempfler✳︎, Jan-Hendrik Lange✳︎, Florian Jug, Corinna Blasse, Eugene W Myers, Bjoern H. Menze, Bjoern Andres
Efficient Algorithms for Moral Lineage Tracing
In: 2017 IEEE International Conference on Computer Vision : ICCV 2017 : proceedings : 22-29 October 2017, Venice, Italy (2017), Piscataway, N.J., IEEE (2017), 4705-4714
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Natalie Dye, Marko Popović, Stephanie Spannl, Raphael Etournay, Dagmar Kainmüller, Suhrid Ghosh, Eugene W Myers, Frank Jülicher, Suzanne Eaton
Cell dynamics underlying oriented growth of the Drosophila wing imaginal disc.
Development, 144(23) 4406-4421 (2017)
DOI
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Martin Weigert, Loic Royer, Florian Jug, Gene Myers
Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks
In: Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2017 : 20th International Conference, Quebec City, QC, Canada, September 10-14, 2017, Proceedings, Part II (2017)(Eds.) Maxime Descoteaux (Lecture Notes in Computer Science ; 10434), Cham, Springer International Publishing (2017), 126-134
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Corinna Blasse, Stephan Saalfeld, Raphael Etournay, Andreas Sagner, Suzanne Eaton, Eugene W Myers
PreMosa: extracting 2D surfaces from 3D microscopy mosaics.
Bioinformatics, 33(16) 2563-2569 (2017)
DOI
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Tobias Boothe, Lennart Hilbert, Michael Heide, Lea Berninger, Wieland B. Huttner, Vasily Zaburdaev, Nadine Vastenhouw, Eugene W Myers, David N. Drechsel, Jochen Rink
A tunable refractive index matching medium for live imaging cells, tissues and model organisms.
Elife, 6 Art. No. e27240 (2017)
Open Access   DOI
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Richard Grunzke✳︎#, Florian Jug✳︎#, Bernd Schuller, René Jäkel, Gene Myers, Wolfgang E Nagel
Seamless HPC Integration of Data-Intensive KNIME Workflows via UNICORE
In: Euro-Par 2016: Parallel Processing Workshops : Euro-Par 2016 International Workshops, Grenoble, France, August 24-26, 2016, Revised Selected Papers (2017)(Eds.) Frédéric Desprez (Lecture Notes in Computer Science ; 10104), Cham, Springer International Publishing (2017), 480-491
DOI
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Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
Sci Rep, 7(1) Art. No. 3935 (2017)
Open Access   DOI
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Djamal Belazzougui, Fabio Cunial, Travis Gagie, Nicola Prezza, Mathieu Raffinot
Flexible indexing of repetitive collections
In: Unveiling Dynamics and Complexity : 13th Conference on Computability in Europe, CiE 2017, Turku, Finland, June 12-16, 2017, Proceedings (2017)(Eds.) Jarkko Kari (Lecture Notes in Computer Science ; 10307), Cham, Springer International Publishing (2017), 162-174
DOI
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Dmitrij Schlesinger✳︎, Florian Jug✳︎, Gene Myers, Carsten Rother, Dagmar Kainmueller
Crowd Sourcing Image Segmentation with iaSTAPLE
In: 14th. IEEE International Symposium on Biomedical Imaging: From Nano to Macro ; ISBI 2017 ; Proceedings (2017)(Eds.) Garry Egan, Piscataway, N.J., IEEE (2017), 401-405
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Martin Weigert, Eugene W Myers, Moritz Kreysing
Biobeam - Rigorous wave-optical simulations of light-sheet microscopy
arXiv, Art. No. arXiv:1706.02261 (2017)
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Jarno Alanko, Fabio Cunial, Djamal Belazzougui, Veli Mäkinen
A framework for space-efficient read clustering in metagenomic samples.
BMC Bioinformatics, 18(Suppl 3) Art. No. 59 (2017)
Open Access   PDF    DOI

2016

Loic Royer, William Lemon, Raghav K Chhetri, Yinan Wan, Michael Coleman, Eugene W Myers, Patrick Keller
Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms.
Nat Biotechnol, 34(12) 1267-1278 (2016)
DOI
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Corinna Blasse
Towards accurate and efficient cell tracking during fly wing development
Ph.D. Thesis,Technische Universität Dresden, Dresden, Germany (2016)
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German Tischler
Low Space External Memory Construction of the Succinct Permuted Longest Common Prefix Array
In: String Processing and Information Retrieval : 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings (2016) Lecture notes in computer science ; 9954, Cham, Springer International Publishing (2016), 178-190
DOI
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Kaiser Matthias, Florian Jug, Olin Silander, Siddharth Deshpande, Thomas Pfohl, Thomas Julou#, Gene Myers#, Erik van Nimwegen#
Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup
bioRxiv, Art. No. 076224 (2016)
Open Access   DOI
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Florian Jug, Evgeny Levinkov, Corinna Blasse, Eugene W Myers, Bjoern Andres
Moral Lineage Tracing
In: Proceedings 29th IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2016) (2016), Piscataway, N.J., IEEE (2016), 5926-5935
DOI
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L Carine Stapel, Benoit Lombardot, Coleman Broaddus, Dagmar Kainmueller, Florian Jug, Eugene W Myers, Nadine Vastenhouw
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.
Development, 143(3) 540-546 (2016)
Open Access   PDF    DOI
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Michael N Economo, Nathan G Clack, Luke D Lavis, Charles R Gerfen, Karel Svoboda, Eugene W Myers, Jayaram Chandrashekar
A platform for brain-wide imaging and reconstruction of individual neurons.
Elife, 5 Art. No. e10566 (2016)
Open Access   PDF    DOI

2015

David Richmond, Dagmar Kainmueller, Ben Glocker, Carsten Rother, Gene Myers
Uncertainty-Driven Forest Predictors for Vertebra Localization and Segmentation
In: Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015 : 18th International Conference, Munich, Germany, October 5-9, 2015, Proceedings, Part I (2015) Lecture Notes in Computer Science ; 9349, Cham, Springer International Publishing (2015), 653-660
DOI
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Yinan Wan, Fuhui Long, Lei Qu, Hang Xiao, Michael Hawrylycz, Eugene W Myers, Hanchuan Peng
BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies.
Neuroinformatics, 13(4) 487-499 (2015)
DOI
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Avinash Patel, Hyun-Ok Kate Lee, Louise Jawerth, Shovamayee Maharana, Marcus Jahnel, Marco Y Hein, Stoyno Stoynov, Julia Mahamid, Shambaditya Saha, Titus Franzmann, Andrei Pozniakovski, Ina Poser, Nicola Maghelli, Loic Royer, Martin Weigert, Eugene W Myers, Stephan W. Grill, David N. Drechsel, Anthony Hyman, Simon Alberti
A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.
Cell, 162(5) 1066-1077 (2015)
DOI
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Loic Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W Myers
ClearVolume: open-source live 3D visualization for light-sheet microscopy.
Nat Methods, 12(6) 480-481 (2015)
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Carlas S Smith, Stephan Preibisch, Aviva Joseph, Sara Abrahamsson, Bernd Rieger, Eugene Myers, Robert H. Singer, David Grunwald
Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking.
J Cell Biol, 209(4) 609-619 (2015)
DOI
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Florian Jug, Tobias Pietzsch, Dagmar Kainmueller, Gene Myers
Tracking by Assignment Facilitates Data Curation
In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014 (2015) IMIC Interactive Medical Image Computing Workshop, Amsterdam, Netherlands, Academic Press (2015), 1-12
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Hanchuan Peng, Eugene W Myers
Constructing 5D developing gene expression patterns without live animal imaging
Biomed Eng Lett, 4(4) 338-346 (2015)
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Eva M Schmid, David Richmond, Daniel A Fletcher
Reconstitution of proteins on electroformed giant unilamellar vesicles.
Methods Cell Biol, 128 319-338 (2015)
DOI
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Raphael Etournay, Marko Popović, Matthias Merkel, Amitabha Nandi, Corinna Blasse, Benoit Aigouy, Holger Brandl, Gene Myers, Guillaume Salbreux, Frank Jülicher, Suzanne Eaton
Interplay of cell dynamics and epithelial tension during morphogenesis of the Drosophila pupal wing.
Elife, 4 Art. No. e07090 (2015)
Open Access   PDF    DOI

2014

Gene Myers
Efficient Alignment Discovery amongst Noisy Long Reads
In: 14th International Workshop, WABI 2014, Wroclaw, Poland, September 8-10, 2014. Proceedings (2014) Lecture Notes in Bioinformatics, Vol. 8701, New York, Springer (2014), 52-67
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Florian Jug, Tobias Pietzsch, Dagmar Kainmueller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine
In: Bayesian and grAphical models for biomedical imaging first international workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers (2014) Lecture Notes in Computer Science ; 8677, New York, Springer (2014), 25-36
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Dagmar Kainmueller, Florian Jug, Carsten Rother, Eugene W Myers
Active Graph Matching for Automatic Joint Segmentation and Annotation of C. elegans
In: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2014 : 17th International Conference, Boston, MA, USA, September 14-18, 2014, Proceedings, Part I (2014) Lecture Notes in Computer Science ; 8673 , New York, Springer (2014), 81-88
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Matthias Merkel, Andreas Sagner, Franz Gruber, Raphael Etournay, Corinna Blasse, Gene Myers, Suzanne Eaton, Frank Jülicher
The Balance of Prickle/Spiny-Legs Isoforms Controls the Amount of Coupling between Core and Fat PCP Systems.
Curr Biol, 24(18) 2111-2123 (2014)
DOI
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Fernando Amat, William Lemon, Daniel P Mossing, Katie McDole, Yinan Wan, Kristin Branson, Eugene W Myers, Patrick Keller
Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data.
Nat Methods, 11(9) 951-958 (2014)
DOI
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Ellie S Heckscher, Fuhui Long, Michael J Layden, Chein-Hui Chuang, Laurina Manning, Jourdain Richart, Joseph C Pearson, Stephen T Crews, Hanchuan Peng, Gene Myers, Chris Q Doe
Atlas-builder software and the eNeuro atlas: resources for developmental biology and neuroscience.
Development, 141(12) 2524-2532 (2014)
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Stephan Preibisch#, Fernando Amat, Evangelia Stamataki, Mihail Sarov, Robert H. Singer, Gene Myers, Pavel Tomancak#
Efficient Bayesian-based multiview deconvolution.
Nat Methods, 11(6) 645-648 (2014)
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Florian Jug✳︎, Tobias Pietzsch✳︎, Stephan Preibisch, Pavel Tomancak
Bioimage Informatics in the context of Drosophila research.
Methods, 68(1) 60-73 (2014)
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Hanchuan Peng, Jianyong Tang, Hang Xiao, Alessandro Bria, Jianlong Zhou, Victoria Butler, Zhi Zhou, Paloma T Gonzalez-Bellido, Seung W Oh, Jichao Chen, Aniruddha Mitra, Richard W Tsien, Hongkui Zeng, Giorgio A Ascoli, Giulio Iannello, Michael Hawrylycz, Eugene Myers, Fuhui Long
Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.
Nat Commun, 5 Art. No. 4342 (2014)
Open Access   PDF    DOI

2013

Jong-Cheol Rah, Erhan Bas, Jennifer Colonell, Yuriy Mishchenko, Bill Karsh, Richard D Fetter, Eugene W Myers, Dmitri B Chklovskii, Karel Svoboda, Timothy D Harris, John T R Isaac
Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography.
Front Neural Circuits, 7 Art. No. 177 (2013)
Open Access   PDF    DOI
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Saket Navlakha✳︎#, Parvez Ahammad✳︎#, Eugene W Myers
Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging.
BMC Bioinformatics, 14 Art. No. 294 (2013)
Open Access   PDF    DOI
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Lorenz Pammer, Daniel T O'Connor, S Andrew Hires, Nathan G Clack, Daniel Huber, Eugene W Myers, Karel Svoboda
The mechanical variables underlying object localization along the axis of the whisker.
J Neurosci, 33(16) 6726-6741 (2013)
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Hung-Hsiang Yu, Takeshi Awasaki, Michaela Schroeder, Fuhui Long, Jacob S Yang, Yisheng He, Peng Ding, Jui-Chun Kao, Gloria Yueh-Yi Wu, Hanchuan Peng, Gene Myers, Tzumin Lee
Clonal development and organization of the adult Drosophila central brain.
Curr Biol, 23(8) 633-643 (2013)
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Fernando Amat, Eugene W Myers, Patrick Keller
Fast and robust optical flow for time-lapse microscopy using super-voxels.
Bioinformatics, 29(3) 373-380 (2013)
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Eugene W Myers
What's behind Blast
In: Models and Algorithms for Genome Evolution (MAGE) (2013) Computational Biology 19, New York, Springer (2013), 3-15
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2012

Arnim Jenett, Gerald M Rubin, Teri-T B Ngo, David Shepherd, Christine Murphy, Heather Dionne, Barret D Pfeiffer, Amanda Cavallaro, Donald Hall, Jennifer Jeter, Nirmala Iyer, Dona Fetter, Joanna H Hausenfluck, Hanchuan Peng, Eric T Trautman, Robert R Svirskas, Eugene W Myers, Zbigniew R Iwinski, Yoshinori Aso, Gina M DePasquale, Adrianne Enos, Phuson Hulamm, Shing Chun Benny Lam, Hsing-Hsi Li, Todd R Laverty, Fuhui Long, Lei Qu, Sean D Murphy, Konrad Rokicki, Todd Safford, Kshiti Shaw, Julie H Simpson, Allison Sowell, Susana Tae, Yang Yu, Christopher T Zugates
A GAL4-driver line resource for Drosophila neurobiology.
Cell Rep, 2(4) 991-1001 (2012)
Open Access   PDF    DOI
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Gene Myers
Why bioimage informatics matters.
Nat Methods, 9(7) 659-660 (2012)
DOI
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Erhan Bas, Eugene Myers, Mustafa G. Uzunbas, Dimitris Metaxsas
Contextual grouping in a concept: a multistage decision strategy for EM segmentation
In: Conference on Bioinformatics and Biomedicine Barcelona, Spain, 2012 (2012), Amsterdam, Netherlands, Academic Press (2012), 1-8
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Jinhyun Kim, Ting Zhao, Ronald S Petralia, Yang Yu, Hanchuan Peng, Eugene Myers, Jeffrey C Magee
mGRASP enables mapping mammalian synaptic connectivity with light microscopy.
Nat Methods, 9(1) 96-102 (2012)
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Nathan G Clack, Daniel T O'Connor, Daniel Huber, Leopoldo Petreanu, Andrew Hires, Simon Peron, Karel Svoboda, Eugene W Myers
Automated tracking of whiskers in videos of head fixed rodents.
PLoS Comput Biol, 8(7) Art. No. e1002591 (2012)
Open Access   PDF    DOI

2011

Min Liu, Hanchuan Peng, Amit K. Roy-Chowdhury, Eugene Myers
3D Neuron Tip Detection in Volumetric Microscopy Images
In: IEEE international Conference on Bioinformatics and Biomedicine (2011), Piscataway, N.J., IEEE (2011), 366-371
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Lei Qu, Fuhui Long, Xiao Liu, Stuart Kim, Eugene Myers, Hanchuan Peng
Simultaneous recognition and segmentation of cells: application in C.elegans.
Bioinformatics, 27(20) 2895-2902 (2011)
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Jun Xie, Ting Zhao, Tzumin Lee, Eugene Myers, Hanchuan Peng
Anisotropic path searching for automatic neuron reconstruction.
Med Image Anal, 15(5) 680-689 (2011)
DOI
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Hanchuan Peng, Fuhui Long, Ting Zhao, Eugene Myers
Proof-editing is the bottleneck of 3D neuron reconstruction: the problem and solutions.
Neuroinformatics, 9(2-3) 103-105 (2011)
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Ting Zhao, Jun Xie#, Fernando Amat#, Nathan G Clack#, Parvez Ahammad#, Hanchuan Peng#, Fuhui Long#, Eugene Myers#
Automated reconstruction of neuronal morphology based on local geometrical and global structural models.
Neuroinformatics, 9(2-3) 247-261 (2011)
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Markus Decker, Steffen Jaensch, Andrei I. Pozniakovsky, Andrea Zinke, Kevin F O'Connell, Wolfgang Zachariae, Eugene Myers, Anthony A. Hyman
Limiting amounts of centrosome material set centrosome size in C. elegans embryos.
Curr Biol, 21(15) 1259-1267 (2011)
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Hanchuan Peng, Phuong Chung, Fuhui Long, Lei Qu, Arnim Jenett, Andrew M Seeds, Eugene W Myers, Julie H Simpson
BrainAligner: 3D registration atlases of Drosophila brains.
Nat Methods, 8(6) 493-500 (2011)
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2010

Jun Xie, Ting Zhao, Tzumin Lee, Eugene Myers, Hanchuan Peng
Automatic neuron tracing in volumetric microscopy images with anisotropic path searching.
In: Medical image computing and computer-assisted intervention - MICCAI 2010 : 13th international conference, Beijing, China, September 20-24, 2010; proceedings, Part II (2010)(Eds.) Tianzi Jiang, Nassir Navab, Josien P. W. Pluim, Max A. Viergever Lecture notes in computer science ; 6362, Dordrecht, Springer (2010), 472-479
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Steffen Jaensch, Markus Decker, Anthony A. Hyman, Eugene Myers
Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos
Bioinformatics, 26(12) 13-20 (2010)
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Hanchuan Peng, Zongcai Ruan, Fuhui Long, Julie H Simpson, Eugene W Myers
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.
Nat Biotechnol, 28(4) 348-353 (2010)
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Daniel T O'Connor, Nathan G Clack, Daniel Huber, Takaki Komiyama, Eugene W Myers, Karel Svoboda
Vibrissa-based object localization in head-fixed mice.
J Neurosci, 30(5) 1947-1967 (2010)
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Shing Chun Benny Lam, Zongcai Ruan, Ting Zhao, Fuhui Long, Arnim Jenett, Julie Simpson, Eugene W Myers, Hanchuan Peng
Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains.
Methods, 50(2) 63-69 (2010)
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Eldar Giladi, John Healy#, Eugene W Myers#, Chris Hart#, Philipp Kapranov#, Doron Lipson#, Steve Roels#, Edward Thayer#, Stan Letovsky#
Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families
J Comput Biol, 17(10) 1279-1293 (2010)
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2009

Xiao Liu, Fuhui Long, Hanchuan Peng, Sarah J Aerni, Min Jiang, Adolfo Sánchez-Blanco, John I Murray, Elicia A. Preston, Barbara Mericle, Serafim Batzoglou, Eugene W Myers, Stuart K Kim
Analysis of cell fate from single-cell gene expression profiles in C. elegans.
Cell, 139(3) 623-633 (2009)
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Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K Kim, Eugene Myers
A 3D digital atlas of C. elegans and its application to single-cell analyses.
Nat Methods, 6(9) 667-672 (2009)
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Hanchuan Peng, Fuhui Long, Eugene W Myers
VANO: a volume-object image annotation system.
Bioinformatics, 25(5) 695-697 (2009)
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2008

Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K Kim, Eugene W Myers
Straightening Caenorhabditis elegans images.
Bioinformatics, 24(2) 234-242 (2008)
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Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K Kim, Gene Myers
Automatic recognition of cells (ARC) for 3D images of C. elegans
In: Proc. 2008 Conf. on Computational Molecular Biology (RECOMB) (Singapore, 2008) (2008) Lecture Notes in Computer Science ; 4955, New York, Springer (2008), 128-139
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2007

David J Begun, Alisha K Holloway#, Kristian Stevens#, LaDeana W Hillier#, Yu-Ping Poh#, Matthew W Hahn#, Phillip M Nista#, Corbin D Jones#, Andrew D Kern#, Colin N Dewey#, Lior Pachter#, Eugene Myers, Charles H Langley#
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
PLoS Biol, 5(11) 310-310 (2007)
Open Access   PDF    DOI
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Christopher D Smith, Robert C Edgar, Mark D Yandell, Douglas R Smith, Susan E Celniker, Eugene W Myers, Gary H Karpen
Improved repeat identification and masking in Dipterans.
Gene, 389(1) 1-9 (2007)
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Michael M Mwangi, Shang Wei Wu#, Yanjiao Zhou#, Krzysztof Sieradzki#, Herminia de Lencastre#, Paul Richardson#, David Bruce#, Edward Rubin#, Eugene W Myers#, Eric D Siggia#, Alexander Tomasz#
Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing
Proc Natl Acad Sci U.S.A., 104(22) 9451-9456 (2007)
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Hanchuan Peng, Fuhui Long, Eugene W Myers
STRAIGHTENING WORM IMAGES
In: Proceedings in 4th IEEE International Symposium on Biomedical Imaging: from Nano to Macro, 2007 : ISBI 2007 ; 12 - 15 April 2007, Arlington, Virginia, USA (2007), Piscataway, N.J., IEEE (2007), 292-295
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Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno
Computability of Models for Sequence Assembly
In: Proceedings in Algorithms in bioinformatics : 7th international workshop, WABI 2007, Philadelphia, PA, USA (2007) Lecture notes in computer science ; 4645, Berlin;Heidelberg, Springer (2007), 289-301
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Fuhui Long, Hanchuan Peng, Eugene W Myers
Automatic Segmentation of Nuclei in 3D Microscopy Images of C. Elegans
In: Proceedings in 4th IEEE International Symposium on Biomedical Imaging: from Nano to Macro (2007), Piscataway, N.J., IEEE (2007), 536-539
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Hanchuan Peng, Fuhui Long, Jie Zhou, Garmay Leung, Michael B Eisen, Eugene W Myers
Automatic image analysis for gene expression patterns of fly embryos.
BMC Cell Biol, 8 Suppl 1 7-7 (2007)
Open Access   PDF    DOI

2006

Tien-Ho Lin, Eugene W Myers, Eric P Xing
Interpreting anonymous DNA samples from mass disasters--probabilistic forensic inference using genetic markers.
Bioinformatics, 22(14) 298-306 (2006)
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Kim R Rasmussen, Jens Stoye, Eugene W Myers
Efficient q-gram filters for finding all epsilon-matches over a given length.
J Comput Biol, 13(2) 296-308 (2006)
PDF    DOI
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Hanchuan Peng, Fuhui Long, Michael B Eisen, Eugene W Myers
Clustering gene expression patterns of fly embryos
In: Proceedings in 3rd IEEE International Symposium on Biomedical Imaging: Macro to Nano (2006), Piscataway, N.J., IEEE (2006), 1144-1147
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2005

Eugene W Myers
The fragment assembly string graph.
Bioinformatics, 21 Suppl 2 79-85 (2005)
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Marcel Margulies, Michael Egholm, William E Altman, Said Attiya, Joel S Bader, Lisa A Bemben, Jan Berka, Michael S Braverman, Yi-Ju Chen, Zhoutao Chen, Scott B Dewell, Lei Du, Joseph M Fierro, Xavier V Gomes, Brian C Godwin, Wen He, Scott Helgesen, Chun Heen Ho, Gerard P Irzyk, Szilveszter C Jando, Maria L I Alenquer, Thomas P Jarvie, Kshama B Jirage, Jong-Bum Kim, James R Knight, Janna R Lanza, John H Leamon, Steven M Lefkowitz, Ming Lei, Jing Li, Kenton L Lohman, Hong Lu, Vinod B Makhijani, Keith E McDade, Michael P McKenna, Eugene W Myers, Elizabeth Nickerson, John R Nobile, Ramona Plant, Bernard P Puc, Michael T Ronan, George T Roth, Gary J Sarkis, Jan Fredrik Simons, John W Simpson, Maithreyan Srinivasan, Karrie R Tartaro, Alexander Tomasz, Kari A Vogt, Greg A Volkmer, Shally H Wang, Yong Wang, Michael P Weiner, Pengguang Yu, Richard F Begley, Jonathan M Rothberg
Genome sequencing in microfabricated high-density picolitre reactors.
Nature, 437(7057) 376-380 (2005)
PDF    DOI
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Robert C Edgar, Eugene W Myers
PILER: identification and classification of genomic repeats.
Bioinformatics, 21 Suppl 1 152-158 (2005)
PDF    DOI
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Roded Sharan, Eugene W Myers
A motif-based framework for recognizing sequence families.
Bioinformatics, 21 Suppl 1 387-393 (2005)
PDF    DOI
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Kim R Rasmussen, Jens Stoye, Eugene W Myers
Efficient q-Gram Filters for Finding All ε-Matches over a Given Length
In: Proceedings in Research in computational molecular biology : 9th annual international conference, RECOMB 2005, Cambridge, MA, USA (2005) Lecture notes in computer science ; 3500, Berlin;Heidelberg, Springer (2005), 189-203
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2004

Sorin Istrail, Granger G Sutton, Liliana Florea, Aaron L. Halpern, C M Mobarry, Ross Lippert, Brian Walenz, Hagit Shatkay, I M Dew, Jason R Miller, M J Flanigan, Nathan J Edwards, R A Bolanos, D P Fasulo, Bjarni V Halldorsson, Sridhar Hannenhalli, Russell Turner, Shibu Yooseph, Fu Lu, D R Nusskern, Bixiong Chris Shue, Xiangqun Holly Zheng, Fei Zhong, A L Delcher, Daniel H. Huson, S A Kravitz, Laurent Mouchard, Knut Reinert, K A Remington, Andrew Clark, Michael S Waterman, Evan E Eichler, Mark D Adams, Michael W Hunkapiller, Eugene W Myers, J C Venter
Whole-genome shotgun assembly and comparison of human genome assemblies.
Proc Natl Acad Sci U.S.A., 101(7) 1916-1921 (2004)
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Gad M Landau, Eugene Myers, Michal Ziv-Ukelson
Two Algorithms for LCS Consecutive Suffix Alignment
In: Proceedings in Combinatorial Pattern Matching : 15th Annual Symposium, CPM 2004, Istanbul, Turkey (2004) Lecture Notes in Computer Science ; 3109, Berlin;Heidelberg, Springer (2004), 173-193
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Hanchuan Peng, Eugene W Myers
Comparing in situ mRNA expression patterns of drosophila embryos
In: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology (2004), New York, ACM (2004), 157-166
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2003

A Bernardo Carvalho, Maria D Vibranovski, Joseph W Carlson, Susan E Celniker, Roger A Hoskins, Gerald M Rubin, Granger G Sutton, Mark D Adams, Eugene W Myers, Andrew Clark
Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome: how far can we go?
Genetica, 117(2-3) 227-237 (2003)
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Mark D Adams, Granger G Sutton, Hamilton O Smith, Eugene W Myers, J C Venter
The independence of our genome assemblies.
Proc Natl Acad Sci U.S.A., 100(6) 3025-3026 (2003)
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Gene Myers, Richard Durbin
A table-driven, full-sensitivity similarity search algorithm.
J Comput Biol, 10(2) 103-117 (2003)
PDF    DOI

2002

Robert A Holt, G Mani Subramanian, Aaron L. Halpern, Granger G Sutton, Rosane Charlab, D R Nusskern, Patrick Wincker, Andrew Clark, José M C Ribeiro, Ron Wides, Steven L Salzberg, Brendan Loftus, Mark D Yandell, William H Majoros, Douglas B Rusch, Zhongwu Lai, Cheryl L Kraft, Josep F Abril, Veronique Anthouard, Peter Arensburger, Peter W Atkinson, Holly Baden, Veronique de Berardinis, Danita Baldwin, Vladimir Benes, Jim Biedler, Claudia Blass, R A Bolanos, Didier Boscus, Mary Barnstead, Shuang Cai, Angela Center, Kabir Chaturverdi, George K Christophides, Mathew A Chrystal, Michele Clamp, Anibal Cravchik, Val Curwen, Ali Dana, A L Delcher, I M Dew, Cheryl A Evans, M J Flanigan, Anne Grundschober-Freimoser, Lisa Friedli, Zhiping Gu, Ping Guan, Roderic Guigo, Maureen E Hillenmeyer, Susanne L Hladun, James R Hogan, Young S Hong, Jeffrey Hoover, Olivier Jaillon, Zhaoxi Ke, Chinnappa Kodira, Elena Kokoza, Anastasios Koutsos, Ivica Letunic, Alex Levitsky, Yong Liang, Jhy-Jhu Lin, Neil F Lobo, John R Lopez, Joel A Malek, Tina C McIntosh, Stephan Meister, Jason Miller, C M Mobarry, Emmanuel Mongin, Sean D Murphy, David A O'Brochta, Cynthia Pfannkoch, Rong Qi, Megan A Regier, K A Remington, Hongguang Shao, Maria V Sharakhova, Cynthia D Sitter, Jyoti Shetty, Thomas J Smith, Renee Strong, Jingtao Sun, Dana Thomasova, Lucas Q Ton, Pantelis Topalis, Zhijian Tu, Maria F Unger, Brian Walenz, Aihui Wang, Jian Wang, Mei Wang, Xuelan Wang, Kerry J Woodford, Jennifer R Wortman, Martin Wu, Alison Yao, Evgeny M Zdobnov, Hongyu Zhang, Qi Zhao, Senming Zhao, Shiaoping C Zhu, Igor Zhimulev, Mario Coluzzi, Alessandra della Torre, Charles W Roth, Christos Louis, Francis Kalush, Richard J Mural, Eugene W Myers, Mark D Adams, Hamilton O Smith, Samuel Broder, Melissa Gardner, Claire M Fraser, Ewan Birney, Peer Bork, Paul T Brey, J Craig Venter, Jean Weissenbach, Fotis C Kafatos, Frank H Collins, Stephen L Hoffman
The genome sequence of the malaria mosquito Anopheles gambiae.
Science, 298(5591) 129-149 (2002)
PDF    DOI
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Daniel H. Huson, Knut Reinert, Eugene W Myers
The greedy path-merging algorithm for contig scaffolding
Journal of the ACM (JACM), 49(5) 603-615 (2002)
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Jeffrey A Bailey, Zhiping Gu, Royden A Clark, Knut Reinert, Rhea V Samonte, Stuart Schwartz, Mark D Adams, Eugene W Myers, Peter W Li, Evan E Eichler
Recent segmental duplications in the human genome.
Science, 297(5583) 1003-1007 (2002)
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Richard J Mural, Mark D Adams, Eugene W Myers, Hamilton O Smith, George L Gabor Miklos, Ron Wides, Aaron L. Halpern, Peter W Li, Granger G Sutton, Joe Nadeau, Steven L Salzberg, Robert A Holt, Chinnappa Kodira, Fu Lu, Lin Chen, Zuoming Deng, Carlos C Evangelista, Weiniu Gan, Thomas J Heiman, Jiayin Li, Zhenya Li, Gennady V Merkulov, Natalia V Milshina, Ashwinikumar K Naik, Rong Qi, Bixiong Chris Shue, Aihui Wang, Jian Wang, Xin Wang, Xianghe Yan, Jane Ye, Shibu Yooseph, Qi Zhao, Liansheng Zheng, Shiaoping C Zhu, Kendra Biddick, R A Bolanos, A L Delcher, I M Dew, D P Fasulo, M J Flanigan, Daniel H. Huson, S A Kravitz, Jason R Miller, C M Mobarry, Knut Reinert, K A Remington, Qinyu Zhang, Xiangqun H Zheng, D R Nusskern, Zhongwu Lai, Yiding Lei, Wenyan Zhong, Alison Yao, Ping Guan, Rui-Ru Ji, Zhiping Gu, Zhen-Yuan Wang, Fei Zhong, Chunlin Xiao, Chia-Chien Chiang, Mark D Yandell, Jennifer R Wortman, Peter G Amanatides, Susanne L Hladun, Eric C Pratts, Jeffery E Johnson, Kristina L Dodson, Kerry J Woodford, Cheryl A Evans, Barry Gropman, Douglas B Rusch, Eli Venter, Mei Wang, Thomas J Smith, Jarrett T Houck, Donald E Tompkins, Charles Haynes, Debbie Jacob, Soo H Chin, David R Allen, Carl E Dahlke, Robert Sanders, Kelvin Li, Xiangjun Liu, Alex Levitsky, William H Majoros, Quan Chen, Ashley C Xia, John R Lopez, Michael T Donnelly, Matthew H Newman, Anna Glodek, Cheryl L Kraft, Marc Nodell, Feroze Ali, Hui-Jin An, Danita Baldwin-Pitts, Karen Y Beeson, Shuang Cai, Mark Carnes, Amy Carver, Parris M Caulk, Angela Center, Yen-Hui Chen, Ming-Lai Cheng, My D Coyne, Michelle Crowder, Steven Danaher, Lionel B Davenport, Raymond Desilets, Susanne M Dietz, Lisa Doup, Patrick Dullaghan, Steven Ferriera, Carl R Fosler, Harold C Gire, Andres Gluecksmann, Jeannine D Gocayne, Jonathan Gray, Brit Hart, Jason Haynes, Jeffrey Hoover, Tim Howland, Chinyere Ibegwam, Mena Jalali, David Johns, Leslie Kline, Daniel S Ma, Steven MacCawley, Anand Magoon, Felecia Mann, David May, Tina C McIntosh, Somil Mehta, Linda Moy, Mee C Moy, Brian J Murphy, Sean D Murphy, Keith A Nelson, Zubeda Nuri, Kimberly A Parker, Alexandre C Prudhomme, Vinita N Puri, Hina Qureshi, John C Raley, Matthew S Reardon, Megan A Regier, Yu-Hui C Rogers, Deanna L Romblad, Jakob Schutz, John L Scott, Richard Scott, Cynthia D Sitter, Michella Smallwood, Andrew Sprague, Erin Stewart, Renee Strong, Ellen Suh, Karena Sylvester, Reginald Thomas, Ni Ni Tint, Christopher Tsonis, Gary Wang, George Wang, Monica S Williams, Sherita M Williams, Sandra M Windsor, Keriellen Wolfe, Mitchell M Wu, Jayshree Zaveri, Kabir Chaturvedi, Andrei E Gabrielian, Zhaoxi Ke, Jingtao Sun, Gangadharan Subramanian, J Craig Venter, Cynthia Pfannkoch, Mary Barnstead, Lisa D Stephenson
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.
Science, 296(5573) 1661-1671 (2002)
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Eugene W Myers, Granger G Sutton, Hamilton O Smith, Mark D Adams, J Craig Venter
On the sequencing and assembly of the human genome.
Proc Natl Acad Sci U.S.A., 99(7) 4145-4146 (2002)
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Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron L. Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.
Genome Biol, 3(12) 85-85 (2002)
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Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron L. Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd R Laverty, Donna M Muzny, Catherine R Nelson, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert R Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.
Genome Biol, 3(12) Art. No. research0079.1–0079.14 (2002)
Open Access   PDF   

2001

J C Venter, M D Adams, E W Myers, P W Li, Richard J Mural, Granger G Sutton, H O Smith, Mark D Yandell, Cheryl A Evans, Robert A Holt, Jeannine D Gocayne, Peter G Amanatides, R M Ballew, Daniel H. Huson, Jennifer R Wortman, Qinyu Zhang, Chinnappa Kodira, X H Zheng, L Chen, M Skupski, G Subramanian, P D Thomas, J Zhang, George L Gabor Miklos, C Nelson, Samuel Broder, Andrew Clark, Joe Nadeau, V A McKusick, N Zinder, A J Levine, R J Roberts, M Simon, C Slayman, Michael W Hunkapiller, R A Bolanos, A L Delcher, I M Dew, D P Fasulo, M J Flanigan, Liliana Florea, Aaron L. Halpern, Sridhar Hannenhalli, S A Kravitz, S Levy, C M Mobarry, Knut Reinert, K A Remington, J Abu-Threideh, E M Beasley, Kendra Biddick, V Bonazzi, R C Brandon, M Cargill, I Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, V Di Francesco, P Dunn, K Eilbeck, Carlos C Evangelista, Andrei E Gabrielian, Weiniu Gan, W Ge, F Gong, Z Gu, Ping Guan, T J Heiman, M E Higgins, Rui-Ru Ji, Z Ke, K A Ketchum, Z Lai, Y Lei, Z Li, J Li, Y Liang, X Lin, F Lu, Gennady V Merkulov, Natalia V Milshina, H M Moore, Ashwinikumar K Naik, V A Narayan, B Neelam, D R Nusskern, Douglas B Rusch, Steven L Salzberg, W Shao, Bixiong Chris Shue, J Sun, Z Wang, A Wang, X Wang, J Wang, M Wei, Ron Wides, C Xiao, C Yan, Alison Yao, Jane Ye, M Zhan, W Zhang, H Zhang, Q Zhao, L Zheng, F Zhong, W Zhong, S Zhu, Senming Zhao, D Gilbert, S Baumhueter, G Spier, Crystal N. Carter, Anibal Cravchik, T Woodage, F Ali, Hui-Jin An, A Awe, Danita Baldwin, Holly Baden, Mary Barnstead, I Barrow, Karen Y Beeson, D Busam, Amy Carver, Angela Center, M L Cheng, L Curry, Steven Danaher, Lionel B Davenport, Raymond Desilets, Susanne M Dietz, Kristina L Dodson, Lisa Doup, Steven Ferriera, N Garg, Andres Gluecksmann, Brit Hart, J Haynes, C Haynes, C Heiner, Susanne L Hladun, D Hostin, Jarrett T Houck, Tim Howland, Chinyere Ibegwam, J Johnson, Francis Kalush, Leslie Kline, S Koduru, A Love, F Mann, David May, S McCawley, T McIntosh, I McMullen, M Moy, L Moy, B Murphy, K Nelson, Cynthia Pfannkoch, Eric C Pratts, V Puri, Hina Qureshi, Matthew S Reardon, R Rodriguez, Y H Rogers, Deanna L Romblad, B Ruhfel, R Scott, Cynthia D Sitter, Michella Smallwood, E Stewart, Renee Strong, E Suh, R Thomas, Ni Ni Tint, S Tse, C Vech, G Wang, J Wetter, S Williams, M Williams, Sandra M Windsor, E Winn-Deen, Keriellen Wolfe, Jayshree Zaveri, K Zaveri, Josep F Abril, R Guigó, M J Campbell, K V Sjolander, B Karlak, A Kejariwal, H Mi, B Lazareva, T Hatton, A Narechania, K Diemer, A Muruganujan, N Guo, S Sato, V Bafna, Sorin Istrail, Ross Lippert, R Schwartz, Brian Walenz, Shibu Yooseph, D Allen, A Basu, J Baxendale, L Blick, M Caminha, J Carnes-Stine, Parris M Caulk, Y H Chiang, My D Coyne, Carl E Dahlke, A Mays, M Dombroski, Michael T Donnelly, D Ely, S Esparham, Carl R Fosler, Harold C Gire, S Glanowski, K Glasser, Anna Glodek, M Gorokhov, K Graham, Barry Gropman, M Harris, J Heil, S Henderson, Jeffrey Hoover, D Jennings, C M Jordan, J Jordan, J Kasha, L Kagan, C Kraft, Alex Levitsky, M Lewis, X Liu, J Lopez, D Ma, William H Majoros, J McDaniel, S Murphy, Matthew H Newman, T Nguyen, N Nguyen, Marc Nodell, S Pan, J Peck, M Peterson, W Rowe, Robert Sanders, J Scott, M Simpson, T Smith, Andrew Sprague, T Stockwell, R Turner, E Venter, M Wang, M Wen, D Wu, M Wu, Ashley C Xia, A Zandieh, X Zhu
The sequence of the human genome.
Science, 291(5507) 1304-1351 (2001)
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Gene Myers
Optimally separating sequences.
Genome Inform, 12 165-174 (2001)
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Daniel H. Huson, Knut Reinert, S A Kravitz, K A Remington, A L Delcher, I M Dew, M J Flanigan, Aaron L. Halpern, Z Lai, C M Mobarry, Granger G Sutton, E W Myers
Design of a compartmentalized shotgun assembler for the human genome.
Bioinformatics, 17 Suppl 1 132-139 (2001)
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Gene Myers
Comparing sequence scaffolds
In: Proceedings of the fifth annual international conference on Computational biology (2001), New York, ACM (2001), 224-230
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Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W Myers
Comparing Assemblies Using Fragments and Mate-Pairs
In: Proceedings in Algorithms in Bioinformatics : First International Workshop, WABI 2001 Århus Denmark (2001) Lecture notes in computer science ; 2149, Berlin;Heidelberg, Springer (2001), 294-306
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2000

M D Adams, Susan E Celniker, Robert A Holt, Cheryl A Evans, Jeannine D Gocayne, Peter G Amanatides, Steven E Scherer, P W Li, Roger A Hoskins, R F Galle, Reed A George, S E Lewis, Stephen Richards, Michael Ashburner, S Henderson, Granger G Sutton, Jennifer R Wortman, Mark D Yandell, Qinyu Zhang, L X Chen, R C Brandon, Y H Rogers, R G Blazej, Mark Champe, B D Pfeiffer, Kenneth Wan, C Doyle, E G Baxter, G Helt, C R Nelson, G L Gabor, Josep F Abril, A Agbayani, Hui-Jin An, C Andrews-Pfannkoch, Danita Baldwin, R M Ballew, A Basu, J Baxendale, L Bayraktaroglu, E M Beasley, Karen Y Beeson, P V Benos, Benjamin P Berman, D Bhandari, S Bolshakov, D Borkova, M R Botchan, J Bouck, P Brokstein, P Brottier, K C Burtis, D Busam, H Butler, E Cadieu, Angela Center, I Chandra, J M Cherry, S Cawley, Carl E Dahlke, Lionel B Davenport, P Davies, B de Pablos, A L Delcher, Zuoming Deng, A Mays, I M Dew, Susanne M Dietz, Kristina L Dodson, Lisa Doup, M Downes, S Dugan-Rocha, B C Dunkov, P Dunn, K J Durbin, Carlos C Evangelista, C Ferraz, Steven Ferriera, W Fleischmann, Carl R Fosler, Andrei E Gabrielian, N Garg, W M Gelbart, K Glasser, Anna Glodek, F Gong, J H Gorrell, Z Gu, Ping Guan, M Harris, N L Harris, D Harvey, T J Heiman, J R Hernandez, Jarrett T Houck, D Hostin, K A Houston, Tim Howland, M H Wei, Chinyere Ibegwam, Mena Jalali, Francis Kalush, Gary H Karpen, Z Ke, J A Kennison, K A Ketchum, B E Kimmel, Chinnappa Kodira, C Kraft, S A Kravitz, D Kulp, Z Lai, P Lasko, Y Lei, Alex Levitsky, J Li, Z Li, Y Liang, X Lin, X Liu, B Mattei, T C McIntosh, M P McLeod, D McPherson, Gennady V Merkulov, Natalia V Milshina, C M Mobarry, J Morris, A Moshrefi, S M Mount, M Moy, B Murphy, L Murphy, Donna M Muzny, D L Nelson, D R Nelson, K A Nelson, K Nixon, D R Nusskern, Joanne M Pacleb, M Palazzolo, G S Pittman, S Pan, J Pollard, V Puri, M G Reese, Knut Reinert, K A Remington, R D Saunders, F Scheeler, H Shen, Bixiong Chris Shue, I Sidén-Kiamos, M Simpson, M Skupski, T Smith, E Spier, A C Spradling, Mark Stapleton, Renee Strong, E Sun, Robert R Svirskas, C Tector, R Turner, E Venter, A H Wang, X Wang, Z Y Wang, D A Wassarman, George Weinstock, Jean Weissenbach, S M Williams, S M WoodageT, K C Worley, D Wu, S Yang, Q A Yao, Jane Ye, R F Yeh, J S Zaveri, M Zhan, G Zhang, Q Zhao, L Zheng, X H Zheng, F N Zhong, W Zhong, X Zhou, S Zhu, X Zhu, H O Smith, Richard A Gibbs, E W Myers, G M Rubin, J C Venter
The genome sequence of Drosophila melanogaster.
Science, 287(5461) 2185-2195 (2000)
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E W Myers, Granger G Sutton, A L Delcher, I M Dew, D P Fasulo, M J Flanigan, S A Kravitz, C M Mobarry, Knut Reinert, K A Remington, Eric Anson, R A Bolanos, H H Chou, C M Jordan, Aaron L. Halpern, S Lonardi, E M Beasley, R C Brandon, L Chen, P J Dunn, Z Lai, Y Liang, D R Nusskern, M Zhan, Qinyu Zhang, X Zheng, G M Rubin, M D Adams, J C Venter
A whole-genome assembly of Drosophila.
Science, 287(5461) 2196-2204 (2000)
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1999

Gene Myers
Whole-Genome DNA Sequencing
Comput Sci Eng, 1(3) 33-43 (1999)
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Gene Myers
A fast bit-vector algorithm for approximate string matching based on dynamic programming
Journal of the ACM (JACM), 46(3) 395-415 (1999)
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Eric Anson, Gene Myers
Algorithms for Whole Genome Shotgun Sequencing
In: Proceedings of the third annual international conference on Computational molecular biology (1999), New York, ACM (1999), 1-9
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Gene Myers
A Dataset Generator for Whole Genome Shotgun Sequencing
In: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology (1999), Heidelberg, Germany, Intelligent Systems for Molecular Biology (1999), 202-210
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1998

S Levy, L Compagnoni, E W Myers, G D Stormo
Xlandscape: the graphical display of word frequencies in sequences.
Bioinformatics, 14(1) 74-80 (1998)
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Eugene W Myers, Paulo Oliva, Katia S. Guimarães
Reporting Exact and Approximate Regular Expression Matches
In: Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching (1998) Lecture Notes in Computer Science ; 1448, New York, Springer (1998), 91-103
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Gad M Landau, Eugene W Myers#, Jeanette P Schmidt#
Incremental String Comparison
SIAM J Sci Comput, 27(2) 557-582 (1998)
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M F Sagot, E W Myers
Identifying satellites and periodic repetitions in biological sequences.
J Comput Biol, 5(3) 539-553 (1998)
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1997

J L Weber, E W Myers
Human whole-genome shotgun sequencing.
Genome Res, 7(5) 401-409 (1997)
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Eric Anson, E W Myers
ReAligner: a program for refining DNA sequence multi-alignments.
J Comput Biol, 4(3) 369-383 (1997)
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Mudita Jain, E W Myers
Algorithms for computing and integrating physical maps using unique probes.
J Comput Biol, 4(4) 449-466 (1997)
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1996

Eugene W Myers, Sanford Selznick#, Zheng Zhang#, Webb Miller#
Progressive Multiple Alignment with Constraints
J Comput Biol, 3(4) 563-572 (1996)
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Gene Myers, Mudita Jain
Going Against the Grain
In: Proceedings of the Third South American Workshop on String Processing : Recife, Brazil (1996), Recife, Brazil, South American Workshop on String Processing (1996), 203-213
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E W Myers
Approximate matching of network expressions with spacers.
J Comput Biol, 3(1) 33-51 (1996)
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Simpath K Kannan, Eugene W Myers
An Algorithm for Locating Non-overlaping Regions of Maximum Alignment Score
SIAM J Sci Comput, 25(3) 648-662 (1996)
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1995

Sun Wu, Udi Manber, Eugene W Myers
A Sub-Quadratic Algorithm for Approximate Regular Expression Matching
J of Algorithms, 19(3) 346-360 (1995)
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James R Knight, Eugene W Myers
Approximate regular expression pattern matching with concave gap penalties
Algorithmica, 14(1) 85-121 (1995)
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Gene Myers
Approximately matching context-free languages.
Inf Process Lett, 54(2) 85-92 (1995)
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James R Knight, Eugene W Myers
Super-Pattern Matching
Algorithmica, 13(1) 211-243 (1995)
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John D. Kececioglu, Eugene W Myers
Combinatorial algorithms for DNA sequence assembly
Algorithmica, 13(1) 7-51 (1995)
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E W Myers
Toward simplifying and accurately formulating fragment assembly.
J Comput Biol, 2(2) 275-290 (1995)
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Gene Myers, Webb Miller
Chaining multiple-alignment fragments in sub-quadratic time
In: Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms (1995), New York, ACM (1995), 38-47
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Mudita Jain, E W Myers
A note on scoring clones given a probe ordering.
J Comput Biol, 2(1) 33-37 (1995)
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1994

Eugene W Myers
A sublinear algorithm for approximate keyword searching
Algorithmica, 12(4) 345-374 (1994)
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Carolyn J Lawrence, S Honda, N W Parrott, T C Flood, L Gu, L Zhang, Mudita Jain, S Larson, E W Myers
The genome reconstruction manager: a software environment for supporting high-throughput DNA sequencing.
Genomics, 23(1) 192-201 (1994)
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1993

Gerhard Mehldau, Gene Myers
A system for pattern matching applications on biosequences.
Comput Appl Biosci, 9(3) 299-314 (1993)
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Udi Manber, Eugene W Myers
Suffix arrays: A new method for on-line string searches
SIAM J Sci Comput, 22(5) 935-948 (1993)
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1992

E W Myers, X Huang
An O (N² log N) restriction map comparison and search algorithm.
Bull Math Biol, 54(4) 599-618 (1992)
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Gene Myers
A Four Russians algorithm for regular expression pattern matching
Journal of the ACM (JACM), 39(2) 432-448 (1992)
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1990

S F Altschul, W Gish, W Miller, E W Myers, D J Lipman
Basic local alignment search tool.
J Mol Biol, 215(3) 403-410 (1990)
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Sun Wu, Udi Manber, Gene Myers, Webb Miller
An O(NP) Sequence Comparison Algorithm
Inf Process Lett, 35(6) 317-323 (1990)
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1989

Eugene W Myers, Webb Miller
Row replacement algorithms for screen editors
ACM Trans Prog Lang and Systems, 11(1) 33-56 (1989)
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E W Myers, W Miller
Approximate matching of regular expressions.
Bull Math Biol, 51(1) 5-37 (1989)
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1988

E W Myers, W Miller
Optimal alignments in linear space.
Comput Appl Biosci, 4(1) 11-17 (1988)
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J D Hall, E W Myers
A software tool for finding locally optimal alignments in protein and nucleic acid sequences.
Comput Appl Biosci, 4(1) 35-40 (1988)
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W Miller, E W Myers
Sequence comparison with concave weighting functions.
Bull Math Biol, 50(2) 97-120 (1988)
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Webb Miller, Eugene Myers
A Simple Row-replacement Method
Softw Pract Exp, 18(7) 597-611 (1988)
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1987

Christopher W. Fraser, Eugene W Myers
An Editor for Revision Control
ACM Trans Prog Lang and Systems, 9(2) 277-295 (1987)
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1986

Eugene W Myers
An O(ND) Difference Algorithm and Its Variations
Algorithmica, 1(1) 251-266 (1986)
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Webb Miller, Eugene W Myers
Side-effects in Automatic File Updating
Softw Pract Exp, 16(9) 809-820 (1986)
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E W Myers, D W Mount
Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.
Nucleic Acids Res, 14(1) 501-508 (1986)
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1985

Eugene Myers
AN O(ElogE+i) EXPECTED TIME ALGORITHM FOR THE PLANAR SEGMENT INTERSECTION PROBLEM
SIAM J Sci Comput, 14(3) 625-637 (1985)
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Webb Miller, Eugene Myers
A File Comparison Program
Softw Pract Exp, 15(11) 1026-1040 (1985)
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1984

Christopher W. Fraser, Eugene W Myers, Alan L. Wendt
Analyzing and Compressing Assembly Code
In: Proceedings of the SIGPLAN symposium on Compiler construction (1984) ACM SIGPLAN Notices, New York, ACM (1984), 117-121
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Eugene W Myers
Efficient applicative data types
In: Proceedings of the 11th ACM SIGACT-SIGPLAN symposium on Principles of programming languages (1984), New York, ACM (1984), 66-75
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1983

Eugene W Myers
An applicative random-access stack
Inf Process Lett, 17(5) 241-248 (1983)
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1981

Leon J. Osterweil, Eugene W Myers
BIGMAC II: A FORTRAN language augmentation tool
In: Proceedings of the 5th international conference on Software engineering (1981), Piscataway, N.J., IEEE (1981), 410-421
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Eugene W Myers
A precise inter-procedural data flow algorithm
In: Proceedings of the 8th ACM SIGPLAN-SIGACT symposium on Principles of programming languages (1981), New York, ACM (1981), 219-230
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1978

Harold N Gabow, Eugene W Myers
FINDING ALL SPANNING TREES OF DIRECTED AND UNDIRECTED GRAPHS
SIAM J Sci Comput, 7(3) 280-287 (1978)
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